Molecular characteristics of fluoroquinolone-resistant Escherichia coli isolated from suckling piglets with colibacillosis

Objectives Colibacillosis is a frequent enteric disease in the pig industry that causes significant economic losses. The objective of this study was to investigate the molecular characteristics of fluoroquinolone (FQ)-resistant E. coli isolates from suckling piglets with colibacillosis. Results A total of 43 FQ-resistant E. coli isolates were tested in this study and all isolates showed multi-drug resistance (MDR) and mutations in quinolone resistance determining regions (gyrA or parC). Especially, FQ-resistant E. coli isolates with double mutations in both gyrA and parC were shown a high FQs minimum inhibitory concentration (≥ 64 mg/L for ciprofloxacin, ≥ 128 mg/L for enrofloxacin, and ≥ 256 mg/L for norfloxacin). Among 43 FQ-resistant E. coli isolates, 12 (27.9%) were showed plasmid-mediated quinolone resistance (PMQR) positive E. coli. Prevalence of PMQR gene, aac(6’)-Ib-cr, qnrS, and qepA, were identified in 7, 3, and 2 E. coli isolates, respectively. We identified the following in PMQR-positive E. coli isolates: the tetracycline resistance genes tetD (12 isolates, 100.0%), tetE (12 isolates, 100.0%), tetA (11 isolates, 91.7%), and tetB (1 isolate, 8.3%); β-lactamases–encoding blaCMY-2 (10 isolates, 83.3%), blaTEM-1 (7 isolates, 58.3%), blaOXA-1 (7 isolates, 58.3%), blaSHV-1 (3 isolates, 16.7%), and blaAAC-2 (1 isolate, 8.3%); and the chloramphenicol resistance genes (10 isolates, 83.3%); the sulfonamide resistance genes sul1 (9 isolates, 75.0%) and sul2 (10 isolates, 83.3%); the aminoglycoside modifying enzyme gene aac(3)-II (2 isolates, 16.7%). The F4 (7 isolates, 58.3%), LT:STb:EAST1 (5 isolates, 41.7%), and paa (3 isolates, 25.0%) were most common fimbrial antigen, combinations of toxin genes, and non-fimbrial adhesins genes, respectively. All PMQR-positive E. coli carried class I integrons but only 4 isolates carried the gene cassette. The most prevalent plasmid replicon was FIB (9 isolates, 75.0%), followed by FIC, HI1, and N (7 isolates, 58.3%), respectively. Conclusions Because FQ-resistant E. coli can serve as a reservoir of FQ resistant genetic determinants that can be transferred to pathogenic bacteria in humans or pigs, this represents a public health hazard. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02632-9.


Background
Colibacillosis caused by Escherichia coli (E. coli) in pigs is the most frequent enteric disease and an important cause of death in suckling piglets [1]. This disease may result in significant economic losses in the pig industry because of mortality, decreased weight gain, and costs for treatments, vaccinations and feed supplements [2]. The use of antimicrobial drugs such as β-lactams, aminoglycosides, Open Access *Correspondence: wklee@cbu.ac.kr and fluoroquinolones (FQs) has remained the primary option for controlling colibacillosis.
FQs are broad-spectrum antimicrobials agents and have been used for the treatment of various infections caused by E. coli or other gram-negative bacteria. The World Health Organization (WHO) has classified FQs as ''critically important antimicrobials'' because of their clinical importance in both human and animal medicine [3]. Because the importance of FQs in humans and animals is increasing, FQ-resistant bacteria are a major concern in the treatment of infectious diseases. Notably, FQ-resistant E. coli have emerged in Korea after enrofloxacin was licensed to be used for veterinary purposes [4].
Multiple mechanisms are involved in resistance to FQ in Enterobacteriaceae. The major mechanisms of resistance to FQ involve mutations of chromosomal genes encoding DNA gyrase and/or topoisomerase IV [5,6]. In addition, three different plasmid-mediated quinolone resistance (PMQR) determinants have been described: qnr-mediated inhibition of quinolone binding to DNA [7,8], qepA encoded efflux pump [9], and the aac(6')-Ib-cr mediated FQ acetylation [10,11]. The PMQR genes confer only low-level resistance to FQ; however, they can be spread horizontally among enterobacteria and facilitate the selection of resistant mutants following exposure to FQ [12]. Although studies from several countries have documented the prevalence and characteristics of FQresistance in healthy pigs [13][14][15], there is still limited information regarding the molecular characteristics of FQ-resistant and PMQR-positive E. coli isolated from suckling piglets with diarrhea. Therefore, the purpose of this study was to investigate the molecular characteristics of FQ-resistant E. coli isolates from suckling piglets with colibacillosis.

Materials and methods
Bacterial isolates E. coli isolates collected from each colibacillosis clinical case in suckling piglets from 2007-2018 were tested. The farms consisted of 42 different pig herds (50 to 100 sows per each herd). The aseptically collected intestinal contents and feces were inoculated on MacConkey agar(BD Biosciences, Sparks, MD) containing 4 mg/mL of ciprofloxacin (CIP; Sigma-Aldrich, St.Louis, MO). Subsequently, suspected E. coli colonies were identified by VITEK II system (bioMéreiux, France). Thus, a total of 43 CIP-resistant E. coli were tested in this study.

O-Serogroup typing
O-serogroup typing was performed using rabbit antisera purchased from SSI (Serum Staten Institute, Denmark) with the slide agglutination technique of the Animal and Plant Quarantine Agency (Gimcheon, Korea). A standard strain was obtained from Dr. J.M. Fairbrother (OIE E. coli Reference Laboratory, Quebec, Canada).

Identification of mutations in quinolone-resistance-determining regions and detection of plasmid-mediated quinolone-resistance genes
PCR was carried out to amplify quinolone resistance determining regions (QRDRs) of the target genes (gyrA, and parC) to identify mutations in 43 FQ-resistant E. coli isolates using primers and conditions described previously [18,19]. The PCR products were purified using GFX PCR DNA and the gel band purification kit (Amersham Bioscience, Freiburg, Germany), and sequenced by an automatic sequencer (Cosmogenetech, Seoul, Korea). The sequences were aligned with those in the GenBank nucleotide database using the Basic Local Alignment Search Tool (BLAST) program available through the National Center for Biotechnology Information website (http:// www. ncbi. nlm. nih. gov/ BLAST). PMQR genes (qnrA, qnrB, qnrC, qnrD, qnrS, aac(6')-Ib-cr, and qepA) were detected by PCR amplification and sequencing analysis, as described in Table S1.

Plasmid replicon typing and detection of integrons and gene cassettes
For plasmid replicon typing and detection of integrons and gene cassettes, PCR was performed using DNA extracted from PMQR-positive E. coli isolates. The primers used in this study targeted 18 different replicons [21] and class 1 and 2 integrons (Table S1.). Gene cassettes were tested for integron-positive isolates. The PCR products of the gene cassettes were sequenced as described above.

Conjugation assay
To determine the transferability of PMQR and other genes, conjugation assays were performed using the broth mating method, with E. coli J53 used as the recipient as previously described [22]. Transconjugants were selected on MacConkey agar (BD Biosciences) plates containing sodium azide (100 µg/ml; Sigma-Aldrich) and ampicillin or tetracycline (100 μg/ml; Sigma-Aldrich).
Transferability was confirmed by antimicrobial susceptibility tests and PCR for molecular analysis as described above.

Antimicrobial resistance
MDR patterns of FQ-resistant E. coli isolates from colibacillosis are shown in Table 1

Discussion
Suckling piglets are vulnerable to colibacillosis for many reasons such as changes in environmental conditions, a decline in maternal antibody titers, and various stresses. Antimicrobials are used in intensive pig production systems to control infectious diseases. In particular, FQs are highly effective antimicrobial class with many advantages including high oral absorption, large volume of distribution, and broad-spectrum antimicrobial activity [23]. However, increasing use of these agents has led to rising rates of resistance to FQs in E. coli worldwide [24]; thus, the probability of treatment failure may be increased [25].
In this study, all FQ-resistant E. coli isolates showed were MDR (resistance to more than six antimicrobial agents) with high levels of resistance to several antimicrobials: aminoglycosides (100.0%), penicillins (100.0%), tetracyclines (97.7%), and phenicols (90.7%). In particular, five isolates showed resistance to more than 10 classes. These results were consistent with previous studies showing coassociation of resistance to other classes of antimicrobials and high MDR rates among FQ-resistant E. coli [26,27]. This occurs because PMQR genes and other antimicrobial-resistance genes are linked together on the plasmid [26].
The O-serogroup is considered one of the major virulence factors of E. coli and variety of O-serogroups has been associated with diarrhea [28][29][30]. In the present study, 17 O-serogroups were detected and O149 was most common. The O149 serogroup has been determined to be the dominant serogroup in cases of diarrhea in many countries including China and Canada [31,32]. In addition, in this study, all isolates (100%) had gyrA mutations, and 29 isolates (67.4%) were double amino acid substitutions (S83L plus substitution in aspartic acid 87). These results were consistent with previous studies showing that DNA gyrase is the primary target of FQ in gram-negative bacteria, and gyrA mutations are dominant mutations in E. coli [33]. Moreover, 37 (86.0%) FQ-resistant E. coli isolates had mutations at codon 80 in parC in the QRDRs, and the most common type of amino-acid substitution was S80I in parC. Previous studies reported that the substitution S80I was most frequently observed among substitutions in the QRDR of parC [34,35]. These results are consistent with those observed in E. coli isolates from humans [36,37]. Also, the MICs ranges of isolates with double mutations in gyrA were relatively higher than those of other isolates with single mutations in gyrA. Notably, FQ-resistant E. coli isolates carrying double mutations in gyrA in combination with double mutations in parC were identified at high levels of MICs (≥ 64 mg/L for CIP, ≥ 128 mg/L for ENR, and ≥ 256 mg/L for NOR). These results are consistent with those of recent studies showing that the total number of point mutations in QRDR was positively correlated with the increased MIC.
In this study, 12 FQ-resistant E. coli isolates carried three types of PMQR genes, aac(6')-Ib-cr (7 isolates), qnrS (3 isolates), and qepA (2 isolates). These PMQR variants have been previously detected in E. coli from livestock, including in healthy animals and retail meats in the Czech Republic [38], China [39], and the United States [40], as well as from swine in Korea [14]. Also, to acquire FQ resistance, bacteria usually require at least double mutations in QRDRs [41]. However, in this study, two isolates (4 mg/L for CIP, 8 mg/L for ENR, and 8 mg/L for NOR) had only a single mutation in gyrA and harbored qnrS in its plasmid. This result showed that PMQR genes play a role in FQ resistance [42].
The rise of antimicrobial resistance is thought to be closely associated with the widespread transfer of resistance genes between bacterial species. In this study, all 12 PMQR-positive E. coli isolates carried a variety of antimicrobial resistance genes such as blaCMY, blaTEM, blaOXA, blaSHV, blaAAC , tetA, tetB, tetD, tetE, aac(3)-II, sul1, sul2, and cmlA and harbored mobile elements such as integrons and gene cassettes at the same time. The bla genes hydrolyze the characteristic β-lactam ring and confer resistance to most β-lactam antimicrobials, including cephalosporins [43]. Previous studies reported that the PMQR genes in bla positive-E. coli were detected at high levels [44]. The presence of the PMQR genes may be significantly associated with the β-lactamase gene, perhaps due to common carriage on a plasmid in Enterobacteriaceae [45]. Also, all 12 PMQR-positive E. coli isolates harbored class 1 integrons and four isolates also contained gene cassettes aadA or dfrA or both genes. These genes are frequently detected in class 1 integrons isolated from animals and humans in Korea [46]. Therefore, integrons in PMQR-positive E. coli isolates from suckling piglets may have acquired the genetic determinants of drug resistance, which could become a concern.
Plasmids are small DNA molecules that are distinct from chromosomes and can provide beneficial effects to bacteria such as antibiotic resistance through horizontal gene transfer [21]. In this study, 10 plasmid replicon types were identified in all 12 PMQR-positive E. coli isolates. The most common plasmid replicon was IncF plasmids including FIB, and FIC. IncF plasmids were associated with the important role in the spread of virulence and resistance to important classes of antimicrobials including quinolones, β-lactams, TEs, sulfonamides, chloramphenicol, and aminoglycosides among Enterobacteriaceae [47].
The detection of E. coli virulence factors is important for diagnosing and establishing preventative measures for colibacillosis [48]. In this study, toxin genes LT, STb, and Sta were detected in nine (75.0%), nine (75.0%), and one (8.3%) PMQR-positive E. coli isolates, respectively. These LT, STa, and STb genes damage the vessel and cause edema and a high mortality in pigs [49]. Also, the most prevalent fimbriae antigen was F4 (7 isolates, 58.3%). F4 fimbriae have been frequently detected in piglets in several countries such as Japan, Europe, and the United States [50][51][52]. Previous studies reported that paa is known to have a high association with F4 [50,53]. In this study, 6 (50.0%) PMQR-positive E. coli isolates were identified as having the paa gene and coexisting with the F4 gene. Although the specific role of the paa gene in the development of pathogenic E. coli has not yet been clearly defined, various virotypes may also appear as a result of horizontal gene transferability of the paa gene [54].

Conclusions
This study investigated the molecular characteristics of FQ-resistant E. coli isolated from suckling piglets with colibacillosis. All FQ-resistant E. coli isolates showed an MDR phenotype, and the most prevalent of the mutations were double point mutations in gyrA and a single mutation in parC. Also, FQ-resistant E. coli isolates with PMQR genes carried various antimicrobial genes and harbored mobile elements and plasmid replicons.
Antimicrobial resistance may become a serious problem because many drugs are probably ineffective for the treatment of colibacillosis and resistance elements can be horizontally transferred on pig farms. Also, this represents a public health hazard because FQ-resistant E. coli can serve as a reservoir of FQ resistant genetic determinants that can be transferred to pathogenic bacteria in humans or pigs. These data support the critical need for comprehensive surveillance of antimicrobial resistance on pig farms.
Additional file 3: Table S2. History of samples and isolates separated from each sample.